; Topology for 16:0 - Sphingomyelin ; ================================= ; Created by Perttu Niemela, 23.6.2003 ; ; 15 17 ; | " ; 1 10 14-16-18-19-20-21-22-23-24-25-26-27-28-29-30-31-32 ; | | | ; 2-4-5-6-7-8-11-12-13 ; | | | ; 3 9 33-36=37-38-39-40-41-42-43-44-45-46-47-48-49-50 ; | ; 34-35 ; ; H O ; | " ; CH3 OM N-C-CH2- ... -CH2-CH3 ; | | | ; CH3-NL-CH2-CH2-OS-P-OS-CH2-CH1 ; | | | ; CH3 OM CH1-CH1=CH1-CH2- ... -CH2-CH3 ; | ; OA-HO ; ; Explanations ; ============ ; - Atom types, charges and masses are from Tielemann's description ; http://moose.bio.ucalgary.ca/files/lipid.itp. Exception: peptide ; bond (atoms 14-17) and the OH-group (34-35) adapted from GROMACS ; force field (ffgmx.itp). ; - Bond/angle parameters are from GROMACS ; - Chain dihedrals from lipid.itp, others from GROMACS ; - C=C double bond from Tielemann's popc.itp [ moleculetype ] ;name nrexcl SM 3 [ atoms ] ; *********************************************************************** ; - Atom types "Lxx" are from Tielemann's lipid.itp, the others (atoms ; 14,15,34,35) are standard GROMACS atoms (ffgmx.atp). ; - Headgroup (atoms 1-12) charges from Tielemann's dppc.itp. ; - Atom nr 13: This kind of carbon exists g.g. in ALA/PRO, charge = 0.0 ; in both cases (ffgmx.rtp) ; - Peptide bond (14-17) charges from ffgmx.rtp ; - OH-group (33-35) charges from 1-lauroyl-glycerol: 1mlg.itp, standard ; building block of GROMACS ; *********************************************************************** ; nr type resnr residu atom cgnr charge ; total charge 1 LC3 1 SM C1 0 0.400 ; 0.400 2 LC3 1 SM C2 0 0.400 ; 0.800 3 LC3 1 SM C3 0 0.400 ; 1.200 4 LNL 1 SM N4 0 -0.500 ; 0.700 5 LH2 1 SM C5 0 0.300 ; 1.000 6 LH2 1 SM C6 0 0.400 ; 1.400 7 LOS 1 SM O7 0 -0.800 ; 0.600 8 LP 1 SM P8 0 1.700 ; 2.300 9 LOM 1 SM O9 0 -0.800 ; 1.500 10 LOM 1 SM O10 0 -0.800 ; 0.700 11 LOS 1 SM O11 0 -0.700 ; 0.000 12 LC2 1 SM C12 1 0.000 ; 0.000 13 LH1 1 SM C13 2 0.000 ; 0.000 14 N 1 SM N14 3 -0.280 ; -0.280 15 H 1 SM H15 3 0.280 ; 0.000 16 LC 1 SM C16 3 0.380 ; 0.380 17 LO 1 SM O17 3 -0.380 ; 0.000 18 LP2 1 SM C18 4 0.000 ; 0.000 19 LP2 1 SM C19 5 0.000 ; 0.000 20 LP2 1 SM C20 6 0.000 ; 0.000 21 LP2 1 SM C21 7 0.000 ; 0.000 22 LP2 1 SM C22 8 0.000 ; 0.000 23 LP2 1 SM C23 9 0.000 ; 0.000 24 LP2 1 SM C24 10 0.000 ; 0.000 25 LP2 1 SM C25 11 0.000 ; 0.000 26 LP2 1 SM C26 12 0.000 ; 0.000 27 LP2 1 SM C27 13 0.000 ; 0.000 28 LP2 1 SM C28 14 0.000 ; 0.000 29 LP2 1 SM C29 15 0.000 ; 0.000 30 LP2 1 SM C30 16 0.000 ; 0.000 31 LP2 1 SM C31 17 0.000 ; 0.000 32 LP3 1 SM C32 18 0.000 ; 0.000 33 LH1 1 SM C33 19 0.150 ; 0.150 34 OA 1 SM O34 19 -0.548 ; -0.398 35 HO 1 SM H35 19 0.398 ; 0.000 36 LH1 1 SM C36 20 0.000 ; 0.000 37 LH1 1 SM C37 21 0.000 ; 0.000 38 LP2 1 SM C38 22 0.000 ; 0.000 39 LP2 1 SM C39 23 0.000 ; 0.000 40 LP2 1 SM C40 24 0.000 ; 0.000 41 LP2 1 SM C41 25 0.000 ; 0.000 42 LP2 1 SM C42 26 0.000 ; 0.000 43 LP2 1 SM C43 27 0.000 ; 0.000 44 LP2 1 SM C44 28 0.000 ; 0.000 45 LP2 1 SM C45 29 0.000 ; 0.000 46 LP2 1 SM C46 30 0.000 ; 0.000 47 LP2 1 SM C47 31 0.000 ; 0.000 48 LP2 1 SM C48 32 0.000 ; 0.000 49 LP2 1 SM C49 33 0.000 ; 0.000 50 LP3 1 SM C50 34 0.000 ; 0.000 [ bonds ] ; *********************************************************************** ; All values were taken from the most corresponding parameters in ; ffgmxbon.itp. The C=C double bond from Tielemann's popc.itp ; *********************************************************************** ; ai aj funct c0 c1 ; bond type (in ffgmxbon) 1 4 1 0.14700 376560. ; NL-CH3 (used: NL-CH2) 2 4 1 0.14700 376560. ; NL-CH3 3 4 1 0.14700 376560. ; NL-CH3 4 5 1 0.14700 376560. ; NL-CH2 5 6 1 0.15300 334720. ; CH2-CH2 6 7 1 0.14300 251040. ; CH2-OS 7 8 1 0.16100 251040. ; OS-P 8 9 1 0.14800 376560. ; P-OM 8 10 1 0.14800 376560. ; P-OM 8 11 1 0.16100 251040. ; P-OS 11 12 1 0.14300 251040. ; OS-CH2 12 13 1 0.15300 334720. ; CH2-CH1 13 14 1 0.14700 376560. ; CH1-N 14 15 1 0.10000 374468. ; N-H 14 16 1 0.13300 418400. ; N-C 16 17 1 0.12300 502080. ; C=0 16 18 1 0.15300 334720. ; C-CH2 18 19 1 0.15300 334720. ; CH2-CH2 19 20 1 0.15300 334720. ; CH2-CH2 20 21 1 0.15300 334720. ; CH2-CH2 21 22 1 0.15300 334720. ; CH2-CH2 22 23 1 0.15300 334720. ; CH2-CH2 23 24 1 0.15300 334720. ; CH2-CH2 24 25 1 0.15300 334720. ; CH2-CH2 25 26 1 0.15300 334720. ; CH2-CH2 26 27 1 0.15300 334720. ; CH2-CH2 27 28 1 0.15300 334720. ; CH2-CH2 28 29 1 0.15300 334720. ; CH2-CH2 29 30 1 0.15300 334720. ; CH2-CH2 30 31 1 0.15300 334720. ; CH2-CH2 31 32 1 0.15300 334720. ; CH2-CH3 13 33 1 0.15300 334720. ; CH1-CH1 33 34 1 0.14300 334720. ; CH1-OA 34 35 1 0.10000 313800. ; OA-HO 33 36 1 0.15300 334720. ; CH1-CH1 36 37 1 0.13900 418400. ; CH1=CH1 (popc.itp) 37 38 1 0.15300 334720. ; CH1-CH2 38 39 1 0.15300 334720. ; CH2-CH2 39 40 1 0.15300 334720. ; CH2-CH2 40 41 1 0.15300 334720. ; CH2-CH2 41 42 1 0.15300 334720. ; CH2-CH2 42 43 1 0.15300 334720. ; CH2-CH2 43 44 1 0.15300 334720. ; CH2-CH2 44 45 1 0.15300 334720. ; CH2-CH2 45 46 1 0.15300 334720. ; CH2-CH2 46 47 1 0.15300 334720. ; CH2-CH2 47 48 1 0.15300 334720. ; CH2-CH2 48 49 1 0.15300 334720. ; CH2-CH2 49 50 1 0.15300 334720. ; CH2-CH3 [ pairs ] ; *********************************************************************** ; Most of the parameters (empty ones) will be taken from lipid.itp, the ; rest (filled in here) were adapted from ffgmxnb.itp. ; *********************************************************************** ; ai aj funct c0 c1 ; pair type in ffgmxnb.itp 1 6 1 2 6 1 3 6 1 4 7 1 5 8 1 6 9 1 6 10 1 6 11 1 7 12 1 8 13 1 9 12 1 10 12 1 11 14 1 0.23473E-02 0.11203E-05 ; OS-N 11 33 1 12 15 1 0.00000E+00 0.00000E+00 ; CH2-H 12 16 1 12 34 1 0.32685E-02 0.22969E-05 ; CH2-OA 12 36 1 13 17 1 13 18 1 13 35 1 0.00000E+00 0.00000E+00 ; CH1-HO 13 37 1 14 19 1 0.33923E-02 0.34700E-05 ; N-CH2 14 34 1 14 36 1 0.26633E-02 0.25147E-05 ; N-CH1 15 17 1 0.00000E+00 0.00000E+00 ; H-O 15 33 1 0.00000E+00 0.00000E+00 ; H-CH2 15 18 1 0.00000E+00 0.00000E+00 ; H-CH2 16 20 1 16 33 1 17 19 1 ; 18 21 1 ; These pairs removed because of the ; 19 22 1 ; type 3 dihedrals ; 20 23 1 ; 21 24 1 ; 22 25 1 ; 23 26 1 ; 24 27 1 ; 25 28 1 ; 26 29 1 ; 27 30 1 ; 28 31 1 ; 29 32 1 33 38 1 34 37 1 0.25662E-02 0.16646E-05 ; OA-CH1 35 36 1 0.00000E+00 0.00000E+00 ; HO-CH1 36 39 1 ; 37 40 1 ; 38 41 1 ; 39 42 1 ; 40 43 1 ; 41 44 1 ; 42 45 1 ; 43 46 1 ; 44 47 1 ; 45 48 1 ; 46 49 1 ; 47 50 1 [ angles ] ; *********************************************************************** ; All values were taken from the most corresponding parameters in ; ffgmxbon.itp (exept for C=C from popc.itp). ; *********************************************************************** ; ai aj ak funct th0 cth ; angletype (ffgmx) 1 4 2 1 109.500 334.720 ; used: H-NL-H 1 4 3 1 109.500 334.720 ; used: H-NL-H 1 4 5 1 109.500 376.560 ; used: H-NL-CH2 2 4 3 1 109.500 334.720 ; used: H-NL-H 2 4 5 1 109.500 376.560 ; used: H-NL-CH2 3 4 5 1 109.500 376.560 ; used: H-NL-CH2 4 5 6 1 109.500 460.240 ; NL-CH2-CH2 5 6 7 1 107.900 460.240 ; CH2-CH2-OS 6 7 8 1 120.000 397.480 ; CH2-OS-P 7 8 9 1 109.600 397.480 ; OS-P-OM 7 8 10 1 109.600 397.480 ; OS-P-OM 7 8 11 1 103.000 397.480 ; OS-P-OS 8 11 12 1 120.000 397.480 ; P-OS-CH2 9 8 10 1 120.000 585.760 ; OM-P-OM 9 8 11 1 109.600 397.480 ; OM-P-OS 10 8 11 1 109.600 397.480 ; OM-P-OS 11 12 13 1 111.000 460.240 ; OS-CH2-CH1 12 13 14 1 109.500 460.240 ; CH2-CH1-N 12 13 33 1 109.500 460.240 ; CH2-CH1-CH2 13 14 15 1 115.000 376.560 ; CH1-N-H 13 14 16 1 122.000 502.080 ; CH1-N-C 13 33 34 1 109.500 460.240 ; CH1-CH1-OA 13 33 36 1 111.000 460.240 ; CH1-CH1-CH1 14 16 17 1 124.000 502.080 ; N-C=O 14 16 18 1 115.000 502.080 ; N-C-CH2 14 13 33 1 109.500 460.240 ; N-CH1-CH2 15 14 16 1 123.000 292.880 ; H-N-C 16 18 19 1 111.000 460.240 ; C-CH2-CH2 17 16 18 1 121.000 502.080 ; O=C-CH2 18 19 20 1 111.000 460.240 ; CH2-CH2-CH2 19 20 21 1 111.000 460.240 ; CH2-CH2-CH2 20 21 22 1 111.000 460.240 ; CH2-CH2-CH2 21 22 23 1 111.000 460.240 ; CH2-CH2-CH2 22 23 24 1 111.000 460.240 ; CH2-CH2-CH2 23 24 25 1 111.000 460.240 ; CH2-CH2-CH2 24 25 26 1 111.000 460.240 ; CH2-CH2-CH2 25 26 27 1 111.000 460.240 ; CH2-CH2-CH2 26 27 28 1 111.000 460.240 ; CH2-CH2-CH2 27 28 29 1 111.000 460.240 ; CH2-CH2-CH2 28 29 30 1 111.000 460.240 ; CH2-CH2-CH2 29 30 31 1 111.000 460.240 ; CH2-CH2-CH2 30 31 32 1 111.000 460.240 ; CH2-CH2-CH3 33 34 35 1 109.500 397.480 ; CH2-OA-HO 33 36 37 1 120.000 502.080 ; CH1-CH1=CH1 (popc.itp) 34 33 36 1 109.500 460.240 ; OA-CH2-CH1 36 37 38 1 120.000 502.080 ; CH1=CH1-CH2 (popc.itp) 37 38 39 1 111.000 460.240 ; CH1-CH2-CH2 38 39 40 1 111.000 460.240 ; CH2-CH2-CH2 39 40 41 1 111.000 460.240 ; CH2-CH2-CH2 40 41 42 1 111.000 460.240 ; CH2-CH2-CH2 41 42 43 1 111.000 460.240 ; CH2-CH2-CH2 42 43 44 1 111.000 460.240 ; CH2-CH2-CH2 43 44 45 1 111.000 460.240 ; CH2-CH2-CH2 44 45 46 1 111.000 460.240 ; CH2-CH2-CH2 45 46 47 1 111.000 460.240 ; CH2-CH2-CH2 46 47 48 1 111.000 460.240 ; CH2-CH2-CH2 47 48 49 1 111.000 460.240 ; CH2-CH2-CH2 48 49 50 1 111.000 460.240 ; CH2-CH2-CH2 [ dihedrals ] ; propers ; *********************************************************************** ; - Most dihedral values taken from ffgmxbon.itp ; - For the chains Ryckaert-Belleman's type "3" dihedral used (parameters ; from lipid.itp) ; *********************************************************************** ; ai aj ak al funct phi0 cp mult ; type in ffgmx 1 4 5 6 1 0.000 3.766 3 ; NL-CH2 4 5 6 7 1 0.000 5.858 3 ; CH2-CH2 5 6 7 8 1 0.000 3.766 3 ; CH2-OS 6 7 8 9 1 0.000 1.046 3 ; OS-P 6 7 8 9 1 0.000 3.138 2 ; OS-P 7 8 11 12 1 0.000 1.046 3 ; P-OS 7 8 11 12 1 0.000 3.138 2 ; P-OS 8 11 12 13 1 0.000 3.766 3 ; OS-CH2 11 12 13 14 1 0.000 5.858 3 ; CH2-CH1 12 13 14 15 1 180.000 0.418 6 ; CH1-N 13 14 16 18 1 180.000 33.472 2 ; N-C 14 16 18 19 1 0.000 0.418 6 ; C-CH2 16 18 19 20 3 ; CH2-CH2 18 19 20 21 3 ; CH2-CH2 19 20 21 22 3 ; CH2-CH2 20 21 22 23 3 ; CH2-CH2 21 22 23 24 3 ; CH2-CH2 22 23 24 25 3 ; CH2-CH2 23 24 25 26 3 ; CH2-CH2 24 25 26 27 3 ; CH2-CH2 25 26 27 28 3 ; CH2-CH2 26 27 28 29 3 ; CH2-CH2 27 28 29 30 3 ; CH2-CH2 28 29 30 31 3 ; CH2-CH2 29 30 31 32 3 ; CH2-CH2 ; 12 13 33 36 1 ; D-erythro-bond -> improper 13 33 34 35 1 0.000 1.255 3 ; CH2-OA 13 33 36 37 1 0.000 5.858 3 ; CH2-CH1 ; 33 36 37 38 1 ; C=C -> improper dihedral 36 37 38 39 1 0.000 5.858 3 ; CH1-CH2 37 38 39 40 3 ; CH2-CH2 38 39 40 41 3 ; CH2-CH2 39 40 41 42 3 ; CH2-CH2 40 41 42 43 3 ; CH2-CH2 41 42 43 44 3 ; CH2-CH2 42 43 44 45 3 ; CH2-CH2 43 44 45 46 3 ; CH2-CH2 44 45 46 47 3 ; CH2-CH2 45 46 47 48 3 ; CH2-CH2 46 47 48 49 3 ; CH2-CH2 47 48 49 50 3 ; CH2-CH2 [ dihedrals ] ; impropers ; *********************************************************************** ; - The values for peptide bond from ffgmx.rtp ; - Carbons 13 and 33 forced in tedraedric conformation and the bond ; between them forced in D-erythro conformation. ; - The C=C double bond adapted from ; http://moose.bio.ucalgary.ca/files/popc.itp ; *********************************************************************** ; ai aj ak al funct q0 cq 16 18 14 17 2 0.000 167.360 ; peptide bond 14 16 13 15 2 0.000 167.360 ; peptide bond 13 12 14 33 2 35.264 334.720 ; tetra-C (from ALA) 33 13 34 36 2 35.264 334.720 ; tetra-C (from 1-lauroyl-glyc) 14 13 34 33 2 0.000 167.360 ; D-erythro 33 38 36 37 2 0.000 167.360 ; CH1=CH1 (trans)